sigima 0.0.1.dev0__py3-none-any.whl → 1.0.0__py3-none-any.whl

sigima/io/image/base.py

@@ -0,0 +1,177 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Image I/O registry
+"""
+
+from __future__ import annotations
+
+import abc
+import os.path as osp
+from typing import Sequence
+
+import numpy as np
+
+from sigima.config import _
+from sigima.io.base import BaseIORegistry, FormatBase
+from sigima.objects.image import ImageObj, create_image
+from sigima.worker import CallbackWorkerProtocol
+
+
+class ImageIORegistry(BaseIORegistry):
+    """Metaclass for registering image I/O handler classes"""
+
+    REGISTRY_INFO: str = _("Image I/O formats")
+
+    _io_format_instances: list[ImageFormatBase] = []
+
+
+class ImageFormatBaseMeta(ImageIORegistry, abc.ABCMeta):
+    """Mixed metaclass to avoid conflicts"""
+
+
+class ImageFormatBase(abc.ABC, FormatBase, metaclass=ImageFormatBaseMeta):
+    """Base image format object.
+
+    This class is used to define the interface for image I/O formats.
+    It is an abstract base class that defines the methods that must be
+    implemented by any image format class.
+    """
+
+    @abc.abstractmethod
+    def read(
+        self, filename: str, worker: CallbackWorkerProtocol | None = None
+    ) -> Sequence[ImageObj]:
+        """Read list of image objects from file
+
+        Args:
+            filename: File name
+            worker: Callback worker object
+
+        Returns:
+            List of image objects
+        """
+
+    @abc.abstractmethod
+    def write(self, filename: str, obj: ImageObj) -> None:
+        """Write data to file
+
+        Args:
+            filename: file name
+            obj: native object (signal or image)
+
+        Raises:
+            NotImplementedError: if format is not supported
+        """
+
+
+class SingleImageFormatBase(ImageFormatBase):
+    """Base image format object for single image (e.g., TIFF, PNG, etc.)."""
+
+    @staticmethod
+    def create_object(filename: str, index: int | None = None) -> ImageObj:
+        """Create empty object
+
+        Args:
+            filename: File name
+            index: Index of object in file
+
+        Returns:
+            Image object
+        """
+        name = osp.basename(filename)
+        if index is not None:
+            name += f" {index:02d}"
+        return create_image(name, metadata={"source": filename})
+
+    def read(
+        self, filename: str, worker: CallbackWorkerProtocol | None = None
+    ) -> list[ImageObj]:
+        """Read list of image objects from file
+
+        Args:
+            filename: File name
+            worker: Callback worker object
+
+        Returns:
+            List of image objects
+        """
+        # Default implementation covers the case of a single image:
+        obj = self.create_object(filename)
+        obj.data = self.read_data(filename)
+        unique_values = np.unique(obj.data)
+        if len(unique_values) == 2:
+            # Binary image: set LUT range to unique values
+            obj.zscalemin, obj.zscalemax = unique_values.tolist()
+        return [obj]
+
+    @staticmethod
+    @abc.abstractmethod
+    def read_data(filename: str) -> np.ndarray:
+        """Read data and return it
+
+        Args:
+            filename: File name
+
+        Returns:
+            Image array data
+        """
+
+    def write(self, filename: str, obj: ImageObj) -> None:
+        """Write data to file
+
+        Args:
+            filename: file name
+            obj: native object (signal or image)
+
+        Raises:
+            NotImplementedError: if format is not supported
+        """
+        data = obj.data
+        self.write_data(filename, data)
+
+    @staticmethod
+    def write_data(filename: str, data: np.ndarray) -> None:
+        """Write data to file
+
+        Args:
+            filename: File name
+            data: Image array data
+        """
+        raise NotImplementedError(f"Writing to {filename} is not supported")
+
+
+class MultipleImagesFormatBase(SingleImageFormatBase):
+    """Base image format object for multiple images (e.g., SIF or SPE).
+
+    Works with read function that returns a NumPy array of 3 dimensions, where
+    the first dimension is the number of images.
+    """
+
+    def read(
+        self, filename: str, worker: CallbackWorkerProtocol | None = None
+    ) -> list[ImageObj]:
+        """Read list of image objects from file
+
+        Args:
+            filename: File name
+            worker: Callback worker object
+
+        Returns:
+            List of image objects
+        """
+        data = self.read_data(filename)
+        if len(data.shape) == 3:
+            objlist = []
+            for idx in range(data.shape[0]):
+                obj = self.create_object(filename, index=idx)
+                obj.data = data[idx, ::]
+                objlist.append(obj)
+                if worker is not None:
+                    worker.set_progress((idx + 1) / data.shape[0])
+                    if worker.was_canceled():
+                        break
+            return objlist
+        obj = self.create_object(filename)
+        obj.data = data
+        return [obj]